Starting phenix.real_space_refine (version: dev) on Sun Feb 19 00:39:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f2o_31429/02_2023/7f2o_31429.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f2o_31429/02_2023/7f2o_31429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f2o_31429/02_2023/7f2o_31429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f2o_31429/02_2023/7f2o_31429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f2o_31429/02_2023/7f2o_31429.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f2o_31429/02_2023/7f2o_31429.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ARG 31": "NH1" <-> "NH2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "D ARG 1": "NH1" <-> "NH2" Residue "R GLU 127": "OE1" <-> "OE2" Residue "R ARG 131": "NH1" <-> "NH2" Residue "R ARG 155": "NH1" <-> "NH2" Residue "R ARG 167": "NH1" <-> "NH2" Residue "R ARG 169": "NH1" <-> "NH2" Residue "R ARG 172": "NH1" <-> "NH2" Residue "R ARG 196": "NH1" <-> "NH2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R ARG 297": "NH1" <-> "NH2" Residue "R ARG 308": "NH1" <-> "NH2" Residue "R ARG 338": "NH1" <-> "NH2" Residue "R ARG 340": "NH1" <-> "NH2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S ARG 18": "NH1" <-> "NH2" Residue "S ARG 67": "NH1" <-> "NH2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "S ARG 191": "NH1" <-> "NH2" Residue "S ARG 202": "NH1" <-> "NH2" Residue "S GLU 222": "OE1" <-> "OE2" Residue "S GLU 234": "OE1" <-> "OE2" Residue "S TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 246": "OE1" <-> "OE2" Residue "Y GLU 22": "OE1" <-> "OE2" Residue "Y GLU 42": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 9004 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1878 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2605 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 76 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 5} Chain: "R" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2308 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 8, 'TRANS': 278} Chain breaks: 1 Chain: "S" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "Y" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 5.46, per 1000 atoms: 0.61 Number of scatterers: 9004 At special positions: 0 Unit cell: (122.265, 109.725, 105.545, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1676 8.00 N 1544 7.00 C 5721 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 130 " - pdb=" SG CYS R 211 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.65 Conformation dependent library (CDL) restraints added in 1.5 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 39.0% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.635A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 229 through 245 removed outlier: 4.069A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.680A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 298 through 318 Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'R' and resid 56 through 85 Proline residue: R 61 - end of helix Processing helix chain 'R' and resid 90 through 119 Proline residue: R 111 - end of helix Processing helix chain 'R' and resid 125 through 160 removed outlier: 4.248A pdb=" N LEU R 129 " --> pdb=" O PHE R 125 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN R 134 " --> pdb=" O CYS R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 195 Proline residue: R 191 - end of helix Processing helix chain 'R' and resid 217 through 233 removed outlier: 3.843A pdb=" N GLU R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 257 Processing helix chain 'R' and resid 264 through 299 Proline residue: R 285 - end of helix Processing helix chain 'R' and resid 303 through 322 removed outlier: 4.253A pdb=" N PHE R 319 " --> pdb=" O GLN R 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 323 through 333 Proline residue: R 329 - end of helix Processing helix chain 'R' and resid 336 through 345 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.030A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 25 Processing helix chain 'Y' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 5.940A pdb=" N LEU A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR A 331 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU A 258 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.321A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.578A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.685A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.594A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.659A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.471A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.218A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 196 through 201 Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.974A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.517A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.517A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 5.158A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG S 191 " --> pdb=" O ASN S 194 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.561A pdb=" N GLN S 231 " --> pdb=" O THR S 238 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR S 238 " --> pdb=" O GLN S 231 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1498 1.32 - 1.44: 2519 1.44 - 1.57: 5081 1.57 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 9191 Sorted by residual: bond pdb=" CA THR A 331 " pdb=" C THR A 331 " ideal model delta sigma weight residual 1.520 1.471 0.049 1.21e-02 6.83e+03 1.64e+01 bond pdb=" C SER A 333 " pdb=" O SER A 333 " ideal model delta sigma weight residual 1.237 1.198 0.038 1.17e-02 7.31e+03 1.08e+01 bond pdb=" CA CYS A 332 " pdb=" C CYS A 332 " ideal model delta sigma weight residual 1.526 1.484 0.042 1.37e-02 5.33e+03 9.59e+00 bond pdb=" C SER A 333 " pdb=" N VAL A 334 " ideal model delta sigma weight residual 1.336 1.309 0.027 1.17e-02 7.31e+03 5.31e+00 bond pdb=" N THR A 331 " pdb=" CA THR A 331 " ideal model delta sigma weight residual 1.457 1.430 0.026 1.24e-02 6.50e+03 4.45e+00 ... (remaining 9186 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.63: 218 106.63 - 113.50: 5002 113.50 - 120.36: 3388 120.36 - 127.23: 3757 127.23 - 134.10: 99 Bond angle restraints: 12464 Sorted by residual: angle pdb=" C ALA R 321 " pdb=" N TYR R 322 " pdb=" CA TYR R 322 " ideal model delta sigma weight residual 122.50 115.11 7.39 1.82e+00 3.02e-01 1.65e+01 angle pdb=" N SER A 333 " pdb=" CA SER A 333 " pdb=" C SER A 333 " ideal model delta sigma weight residual 111.28 115.63 -4.35 1.09e+00 8.42e-01 1.59e+01 angle pdb=" C VAL A 334 " pdb=" N ASP A 335 " pdb=" CA ASP A 335 " ideal model delta sigma weight residual 121.02 126.40 -5.38 1.48e+00 4.57e-01 1.32e+01 angle pdb=" N VAL A 334 " pdb=" CA VAL A 334 " pdb=" C VAL A 334 " ideal model delta sigma weight residual 113.07 117.83 -4.76 1.36e+00 5.41e-01 1.23e+01 angle pdb=" C THR A 331 " pdb=" CA THR A 331 " pdb=" CB THR A 331 " ideal model delta sigma weight residual 109.70 104.84 4.86 1.81e+00 3.05e-01 7.21e+00 ... (remaining 12459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 5037 17.68 - 35.36: 353 35.36 - 53.05: 42 53.05 - 70.73: 11 70.73 - 88.41: 8 Dihedral angle restraints: 5451 sinusoidal: 2115 harmonic: 3336 Sorted by residual: dihedral pdb=" CA TYR R 322 " pdb=" C TYR R 322 " pdb=" N SER R 323 " pdb=" CA SER R 323 " ideal model delta harmonic sigma weight residual 180.00 149.03 30.97 0 5.00e+00 4.00e-02 3.84e+01 dihedral pdb=" CA TYR S 190 " pdb=" C TYR S 190 " pdb=" N ARG S 191 " pdb=" CA ARG S 191 " ideal model delta harmonic sigma weight residual 180.00 153.66 26.34 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 153.69 26.31 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 5448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 931 0.034 - 0.069: 330 0.069 - 0.103: 112 0.103 - 0.138: 40 0.138 - 0.172: 5 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CA SER A 333 " pdb=" N SER A 333 " pdb=" C SER A 333 " pdb=" CB SER A 333 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.42e-01 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA TYR R 322 " pdb=" N TYR R 322 " pdb=" C TYR R 322 " pdb=" CB TYR R 322 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.17e-01 ... (remaining 1415 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 150 " -0.066 9.50e-02 1.11e+02 3.93e-02 8.91e+00 pdb=" NE ARG B 150 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 150 " -0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG B 150 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG B 150 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 228 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.72e+00 pdb=" C LEU R 228 " 0.051 2.00e-02 2.50e+03 pdb=" O LEU R 228 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN R 229 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 230 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C VAL R 230 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL R 230 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL R 231 " 0.017 2.00e-02 2.50e+03 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 492 2.74 - 3.28: 9670 3.28 - 3.82: 15606 3.82 - 4.36: 19245 4.36 - 4.90: 32608 Nonbonded interactions: 77621 Sorted by model distance: nonbonded pdb=" NZ LYS A 210 " pdb=" OD2 ASP B 228 " model vdw 2.194 2.520 nonbonded pdb=" NE ARG A 205 " pdb=" OD1 ASP B 186 " model vdw 2.249 2.520 nonbonded pdb=" NH2 ARG A 208 " pdb=" OD1 ASP A 239 " model vdw 2.264 2.520 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.284 2.440 nonbonded pdb=" O ALA R 158 " pdb=" OG1 THR R 162 " model vdw 2.285 2.440 ... (remaining 77616 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5721 2.51 5 N 1544 2.21 5 O 1676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.520 Check model and map are aligned: 0.130 Process input model: 27.330 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.090 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9191 Z= 0.174 Angle : 0.574 7.394 12464 Z= 0.341 Chirality : 0.043 0.172 1418 Planarity : 0.006 0.081 1580 Dihedral : 12.794 88.412 3290 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.24), residues: 1130 helix: -0.18 (0.23), residues: 410 sheet: -0.65 (0.31), residues: 270 loop : -0.47 (0.30), residues: 450 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 287 time to evaluate : 1.101 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 291 average time/residue: 0.9161 time to fit residues: 289.0472 Evaluate side-chains 256 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 1.070 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.4784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 338 ASN B 125 ASN B 237 ASN ** R 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 ASN ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN S 194 ASN Y 18 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 9191 Z= 0.253 Angle : 0.618 8.876 12464 Z= 0.323 Chirality : 0.044 0.187 1418 Planarity : 0.005 0.039 1580 Dihedral : 5.478 36.598 1248 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1130 helix: 1.70 (0.25), residues: 398 sheet: -0.56 (0.31), residues: 271 loop : 0.05 (0.31), residues: 461 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 284 time to evaluate : 1.037 Fit side-chains outliers start: 33 outliers final: 9 residues processed: 294 average time/residue: 0.9522 time to fit residues: 303.1473 Evaluate side-chains 269 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 260 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.1627 time to fit residues: 2.5261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 91 optimal weight: 0.0670 chunk 101 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 125 ASN B 220 GLN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 ASN ** R 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 9191 Z= 0.236 Angle : 0.581 8.267 12464 Z= 0.305 Chirality : 0.043 0.174 1418 Planarity : 0.004 0.036 1580 Dihedral : 5.112 34.529 1248 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 3.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1130 helix: 2.07 (0.25), residues: 394 sheet: -0.69 (0.30), residues: 270 loop : 0.12 (0.31), residues: 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 264 time to evaluate : 1.136 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 17 residues processed: 282 average time/residue: 0.9727 time to fit residues: 297.0451 Evaluate side-chains 272 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 255 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 7 average time/residue: 0.1190 time to fit residues: 2.7035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN B 110 ASN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 ASN ** R 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN S 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 9191 Z= 0.231 Angle : 0.573 8.044 12464 Z= 0.300 Chirality : 0.043 0.172 1418 Planarity : 0.004 0.044 1580 Dihedral : 4.916 34.014 1248 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1130 helix: 2.11 (0.25), residues: 394 sheet: -0.76 (0.29), residues: 273 loop : 0.12 (0.30), residues: 463 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 263 time to evaluate : 1.075 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 17 residues processed: 277 average time/residue: 0.9842 time to fit residues: 295.1828 Evaluate side-chains 271 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 254 time to evaluate : 1.027 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 8 residues processed: 11 average time/residue: 0.1265 time to fit residues: 3.6876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN B 110 ASN B 125 ASN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 ASN ** R 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 328 ASN S 167 HIS S 186 GLN S 194 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 9191 Z= 0.254 Angle : 0.578 7.866 12464 Z= 0.301 Chirality : 0.043 0.173 1418 Planarity : 0.004 0.053 1580 Dihedral : 4.909 33.470 1248 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 4.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1130 helix: 2.03 (0.25), residues: 394 sheet: -0.71 (0.29), residues: 270 loop : 0.12 (0.30), residues: 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 263 time to evaluate : 1.010 Fit side-chains outliers start: 43 outliers final: 24 residues processed: 285 average time/residue: 0.9506 time to fit residues: 293.9954 Evaluate side-chains 281 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 257 time to evaluate : 1.073 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 13 residues processed: 12 average time/residue: 0.2007 time to fit residues: 4.9487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 20.0000 chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 0.0000 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN B 119 ASN B 237 ASN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN S 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 9191 Z= 0.228 Angle : 0.573 7.981 12464 Z= 0.298 Chirality : 0.043 0.170 1418 Planarity : 0.004 0.042 1580 Dihedral : 4.838 32.791 1248 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 3.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1130 helix: 2.03 (0.25), residues: 394 sheet: -0.71 (0.29), residues: 268 loop : 0.17 (0.30), residues: 468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 258 time to evaluate : 1.067 Fit side-chains outliers start: 31 outliers final: 16 residues processed: 275 average time/residue: 1.0640 time to fit residues: 314.7670 Evaluate side-chains 268 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 252 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 6 average time/residue: 0.2987 time to fit residues: 3.8380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN B 125 ASN B 313 ASN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 9191 Z= 0.259 Angle : 0.596 8.310 12464 Z= 0.310 Chirality : 0.044 0.167 1418 Planarity : 0.004 0.044 1580 Dihedral : 4.855 32.408 1248 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 3.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1130 helix: 1.95 (0.25), residues: 394 sheet: -0.65 (0.30), residues: 267 loop : 0.13 (0.30), residues: 469 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 258 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 22 residues processed: 279 average time/residue: 1.0414 time to fit residues: 313.1566 Evaluate side-chains 274 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 252 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 15 residues processed: 8 average time/residue: 0.3882 time to fit residues: 5.0609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 95 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 359 ASN B 230 ASN B 239 ASN B 295 ASN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 ASN ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN S 194 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9191 Z= 0.228 Angle : 0.592 8.940 12464 Z= 0.305 Chirality : 0.043 0.162 1418 Planarity : 0.004 0.043 1580 Dihedral : 4.802 32.105 1248 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1130 helix: 1.97 (0.25), residues: 394 sheet: -0.63 (0.29), residues: 280 loop : 0.21 (0.30), residues: 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 244 time to evaluate : 1.088 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 19 residues processed: 262 average time/residue: 1.1244 time to fit residues: 316.7921 Evaluate side-chains 262 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 243 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 14 residues processed: 5 average time/residue: 0.6475 time to fit residues: 5.2442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 324 HIS B 230 ASN B 239 ASN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 9191 Z= 0.266 Angle : 0.629 10.375 12464 Z= 0.321 Chirality : 0.045 0.189 1418 Planarity : 0.004 0.043 1580 Dihedral : 4.872 31.467 1248 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.25), residues: 1130 helix: 1.82 (0.25), residues: 394 sheet: -0.67 (0.30), residues: 265 loop : 0.14 (0.30), residues: 471 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 233 time to evaluate : 1.129 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 17 residues processed: 253 average time/residue: 1.0316 time to fit residues: 281.6984 Evaluate side-chains 248 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 231 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 4 average time/residue: 0.3512 time to fit residues: 3.2344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 112 optimal weight: 0.0040 chunk 103 optimal weight: 0.9990 chunk 89 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN B 239 ASN B 295 ASN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 9191 Z= 0.225 Angle : 0.628 11.733 12464 Z= 0.319 Chirality : 0.044 0.230 1418 Planarity : 0.004 0.059 1580 Dihedral : 4.801 31.021 1248 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1130 helix: 1.83 (0.25), residues: 394 sheet: -0.59 (0.31), residues: 263 loop : 0.11 (0.30), residues: 473 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 239 time to evaluate : 1.087 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 18 residues processed: 252 average time/residue: 1.0977 time to fit residues: 297.3207 Evaluate side-chains 252 residues out of total 1000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 234 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 7 average time/residue: 0.4167 time to fit residues: 4.9235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 89 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 16 optimal weight: 0.0170 chunk 78 optimal weight: 0.7980 chunk 5 optimal weight: 0.0980 chunk 64 optimal weight: 0.8980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 237 ASN B 239 ASN B 295 ASN ** R 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Y 18 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.158718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.141113 restraints weight = 11767.079| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.89 r_work: 0.3679 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9191 Z= 0.201 Angle : 0.610 11.419 12464 Z= 0.309 Chirality : 0.044 0.232 1418 Planarity : 0.004 0.044 1580 Dihedral : 4.737 30.749 1248 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1130 helix: 1.80 (0.25), residues: 394 sheet: -0.54 (0.31), residues: 252 loop : 0.17 (0.29), residues: 484 =============================================================================== Job complete usr+sys time: 4612.07 seconds wall clock time: 82 minutes 42.89 seconds (4962.89 seconds total)